Closed campmlc closed 3 years ago
I think those are all about 3 clicks, so I'm not sure how they could be simplified.
Automation should be technically trivial (although error handling would require some work) but would essentially involve "approving" data which you can't see (because it's in a separate not-parts bulkloader). I'm not sure that's a problem, but it is something which everyone should be aware of if we go this route.
This needs to somehow be incorporated into the record checks of the main bulkload file before marking to load. Right now we have to wait for the main file to load and then go back into to several different batch tool bulkoaders to independently check and load these as separate data, if I understand correctly. And this us not being done. At the very least we need clear documentation and instructions to alter our workflow to make this happen.
On Oct 9, 2017 12:02 PM, "dustymc" notifications@github.com wrote:
I think those are all about 3 clicks, so I'm not sure how they could be simplified.
Automation should be technically trivial (although error handling would require some work) but would essentially involve "approving" data which you can't see (because it's in a separate not-parts bulkloader). I'm not sure that's a problem, but it is something which everyone should be aware of if we go this route.
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Here is an example of a record with data that still needs to be loaded. How do we make this happen? http://arctos.database.museum/guid/MSB:Mamm:291916
How do we make this happen?
You tell me....
You can load the extra bits from the parts/IDs/whatever loaders, I can auto-load it for you when the specimen pops in, I can send you emails when there's stuff hanging out in the individual loaders, or when the specimen pops in for that stuff, or WHATEVER.
My concerns revolve around review/approval - I don't like the idea of magicking in data that you probably haven't seen. The individual loaders are normalized to the specimen record, so there's no limit on the number of times a student may have clicked an "add another..." button etc.
Should we add this to the AWG agenda?
Yes, please.
On Tue, Feb 20, 2018 at 3:00 PM, dustymc notifications@github.com wrote:
How do we make this happen?
You tell me....
You can load the extra bits from the parts/IDs/whatever loaders, I can auto-load it for you when the specimen pops in, I can send you emails when there's stuff hanging out in the individual loaders, or when the specimen pops in for that stuff, or WHATEVER.
My concerns revolve around review/approval - I don't like the idea of magicking in data that you probably haven't seen. The individual loaders are normalized to the specimen record, so there's no limit on the number of times a student may have clicked an "add another..." button etc.
Should we add this to the AWG agenda?
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Elevating priority because https://github.com/ArctosDB/arctos/issues/1273#issuecomment-382092450
EnterData/Bulkloader/Browse and Edit now has an "Extras" option which displays linked data.
EnterData/Bulkloader/Browse and Edit -->AJAX has a new column with a count of linked data. Clicking it opens a summary.
New direction: add this stuff to the core bulkloader
20 parts 20 attributes 2 part attributes for all
make data entry form data-driven - there's one more row for (parts and such) until you run out
How do we deal with the existing backlog of identifiers/parts etc. that are in Arctos with a uuid? For example: https://arctos.database.museum/guid/MSB:Mamm:299193
When I go to the bulkload identifiers tool, and click "Manage Existing Data", I have zero records. If I click "check for records entered by people in your collection(s)", I see some records but not all these legacy ones. What am I missing?
You're not missing anything, that's the correct procedure, that UUID is not used for any otherIDs (or anything else).
As far as what SHOULD happen, you tell me.
This will find any "extras" by UUID. Just replace the UUID with the one you want and paste it in to Reports/WriteSQL.
select USERNAME,count(*) c ,'cf_temp_specevent' tbl from cf_temp_specevent where UUID='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
union
select USERNAME,count(*) c ,'cf_temp_parts' tbl from cf_temp_parts where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
union
select USERNAME,count(*) c ,'cf_temp_attributes' tbl from cf_temp_attributes where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
union
select USERNAME,count(*) c ,'cf_temp_oids' tbl from cf_temp_oids where EXISTING_OTHER_ID_NUMBER='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
union
select USERNAME,count(*) c ,'cf_temp_collector' tbl from cf_temp_collector where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
no rows selected
Here's one that finds something.
select USERNAME,count(*) c ,'cf_temp_specevent' tbl from cf_temp_specevent where UUID='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
union
select USERNAME,count(*) c ,'cf_temp_parts' tbl from cf_temp_parts where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
union
select USERNAME,count(*) c ,'cf_temp_attributes' tbl from cf_temp_attributes where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
union
select USERNAME,count(*) c ,'cf_temp_oids' tbl from cf_temp_oids where EXISTING_OTHER_ID_NUMBER='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
union
select USERNAME,count(*) c ,'cf_temp_collector' tbl from cf_temp_collector where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
here's everything in the temp tables - not all of it will have a UUID, most is probably just pending or completed-and-undeleted loads.
create table temp_pending_extras as
select USERNAME,count(*) c ,'cf_temp_specevent' tbl from cf_temp_specevent group by username
union
select USERNAME,count(*) c ,'cf_temp_parts' tbl from cf_temp_parts group by username
union
select USERNAME,count(*) c ,'cf_temp_attributes' tbl from cf_temp_attributes group by username
union
select USERNAME,count(*) c ,'cf_temp_oids' tbl from cf_temp_oids group by username
union
select USERNAME,count(*) c ,'cf_temp_collector' tbl from cf_temp_collector group by username
;
You can use ManageArctos/DeveloperTools/CSVFromTable to download any table - eg, cf_temp_attributes.
I'm afraid I don't understand any of those options. I realize it would be very useful for me to learn SQL, but I've resisted because I think the majority of Arctos operators would highly resist having to learn it, and the tools need to be able to accommodate everyone.
I'm confused as to why that UUID exists if it isn't used for anything. Are students entering UUIDs by accident? There must have been some data someone was trying to link, and if there is nothing out there to load, something must have gotten lost. We have a lot of these.
On Fri, May 11, 2018 at 10:12 AM, dustymc notifications@github.com wrote:
You're not missing anything, that's the correct procedure, that UUID is not used for any otherIDs (or anything else).
As far as what SHOULD happen, you tell me.
This will find any "extras" by UUID. Just replace the UUID with the one you want and paste it in to Reports/WriteSQL.
select USERNAME,count() c ,'cf_temp_specevent' tbl from cf_temp_specevent where UUID='b16caab2-e272-4019-8eec-d6b8461607ee' group by username union select USERNAME,count() c ,'cf_temp_parts' tbl from cf_temp_parts where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username union select USERNAME,count() c ,'cf_temp_attributes' tbl from cf_temp_attributes where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username union select USERNAME,count() c ,'cf_temp_oids' tbl from cf_temp_oids where EXISTING_OTHER_ID_NUMBER='b16caab2-e272-4019-8eec-d6b8461607ee' group by username union select USERNAME,count(*) c ,'cf_temp_collector' tbl from cf_temp_collector where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
no rows selected
Here's one that finds something.
select USERNAME,count() c ,'cf_temp_specevent' tbl from cf_temp_specevent where UUID='b16caab2-e272-4019-8eec-d6b8461607ee' group by username union select USERNAME,count() c ,'cf_temp_parts' tbl from cf_temp_parts where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username union select USERNAME,count() c ,'cf_temp_attributes' tbl from cf_temp_attributes where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username union select USERNAME,count() c ,'cf_temp_oids' tbl from cf_temp_oids where EXISTING_OTHER_ID_NUMBER='b16caab2-e272-4019-8eec-d6b8461607ee' group by username union select USERNAME,count(*) c ,'cf_temp_collector' tbl from cf_temp_collector where other_id_number='b16caab2-e272-4019-8eec-d6b8461607ee' group by username
[image: screen shot 2018-05-11 at 9 03 52 am] https://user-images.githubusercontent.com/5720791/39934311-41d87582-54fa-11e8-826a-de3aca604e09.png
here's everything in the temp tables - not all of it will have a UUID, most is probably just pending or completed-and-undeleted loads.
create table temp_pending_extras as select USERNAME,count() c ,'cf_temp_specevent' tbl from cf_temp_specevent group by username union select USERNAME,count() c ,'cf_temp_parts' tbl from cf_temp_parts group by username union select USERNAME,count() c ,'cf_temp_attributes' tbl from cf_temp_attributes group by username union select USERNAME,count() c ,'cf_temp_oids' tbl from cf_temp_oids group by username union select USERNAME,count(*) c ,'cf_temp_collector' tbl from cf_temp_collector group by username ;
temp_pending_extras.csv.zip https://github.com/ArctosDB/arctos/files/1996072/temp_pending_extras.csv.zip
You can use ManageArctos/DeveloperTools/CSVFromTable to download any table - eg, cf_temp_attributes.
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Agreed in principle, but we'll never have an infinite number of tools to do the infinite number of things that can be done in Arctos!
I'm happy to help you SQL-shuffle things around - eg, if you want to "claim" everything from your users in the CSV I provided or whatever.
Or you can just go through the "claim from my users" process for each of the half-dozen things the bulkloader can write to - that's all the SQL is doing.
UUIDs exist because they were or might have been handy for something - they're just a unique(ish) identifier that can be created at any time. They're in specimen records because someone loaded them (eg, to help find stuff in iDigBio) or because something needs to or already has (or was going to but then was deleted) go in asynchronously, or maybe just because someone clicked the button to see what would happen.
Can I claim everything from MSB users, so I can see what is going on and how to resolve? I'm pretty sure no one else has any idea of what to do. MSB Mammals has had to create these through student data entry to accommodate extra attributes, parts, and IDs that won't fit in the standard form. They've been doing this for a couple of years, and I don't think any of the UUIDs so created have been resolved to link to the corresponding data. It would be good to figure out what records have these so we can go back and find out if data were lost and need to be re-entered.
On Fri, May 11, 2018 at 11:42 AM, dustymc notifications@github.com wrote:
Agreed in principle, but we'll never have an infinite number of tools to do the infinite number of things that can be done in Arctos!
I'm happy to help you SQL-shuffle things around - eg, if you want to "claim" everything from your users in the CSV I provided or whatever.
Or you can just go through the "claim from my users" process for each of the half-dozen things the bulkloader can write to - that's all the SQL is doing.
UUIDs exist because they were or might have been handy for something - they're just a unique(ish) identifier that can be created at any time. They're in specimen records because someone loaded them (eg, to help find stuff in iDigBio) or because something needs to or already has (or was going to but then was deleted) go in asynchronously, or maybe just because someone clicked the button to see what would happen.
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Can I claim everything from MSB users, so I can see what is going on and how to resolve?
You have manage_collection, so you can claim anything from anyone with access to any of the collections to which you have access. (That includes me and Carla and anyone else who needs that access for various reasons.) Here's everybody with something that MIGHT be your data - let me know what usernames are "yours" and we can go from there.
UAM@ARCTOS> select distinct username from temp_pending_extras;
BIOKIDRICHY ELAINEPERRY LEAC LFREDERICK RABZ711 TORIVIOLA TRUCKEY
ACDOLL ACHINN KKMILLS NOCHOA5 SMLADINICH CAMPMLC CWITT DLM JEGELEWICZ KATOBLER LBOLLING PBHAKTA SIERRALROMERO SOMIYADUNNUM VKOOMSON ANDY CWLINKEM MROBINSON AJLINN1910 DEMBOSKI SALTAMIRANO SARA SHANNONOBRIEN EJOHNSON CCICERO EBRAKER FSKBH1 JMALEY1 KGUTIERREZ KOLSON36 MAVERY TEAHAMIRKABIRIAN ALEXANDERO SLIPHARDT
Mariel, let me know if there is anything you want me to help with on this. Most of the MSB users are mammals students.
Jonathan L. Dunnum Ph.D. Senior Collection Manager Division of Mammals, Museum of Southwestern Biology University of New Mexico Albuquerque, NM 87131 (505) 277-9262 Fax (505) 277-1351
MSB Mammals website: http://www.msb.unm.edu/mammals/index.html Facebook: http://www.facebook.com/MSBDivisionofMammals
Shipping Address: Museum of Southwestern Biology Division of Mammals University of New Mexico CERIA Bldg 83, Room 204 Albuquerque, NM 87131
From: Mariel Campbell notifications@github.com Sent: Friday, May 11, 2018 11:51:27 AM To: ArctosDB/arctos Cc: Jonathan Dunnum; Assign Subject: Re: [ArctosDB/arctos] Auto-upload extra identifiers, attributes from data entry (#1294)
Can I claim everything from MSB users, so I can see what is going on and how to resolve? I'm pretty sure no one else has any idea of what to do. MSB Mammals has had to create these through student data entry to accommodate extra attributes, parts, and IDs that won't fit in the standard form. They've been doing this for a couple of years, and I don't think any of the UUIDs so created have been resolved to link to the corresponding data. It would be good to figure out what records have these so we can go back and find out if data were lost and need to be re-entered.
On Fri, May 11, 2018 at 11:42 AM, dustymc notifications@github.com wrote:
Agreed in principle, but we'll never have an infinite number of tools to do the infinite number of things that can be done in Arctos!
I'm happy to help you SQL-shuffle things around - eg, if you want to "claim" everything from your users in the CSV I provided or whatever.
Or you can just go through the "claim from my users" process for each of the half-dozen things the bulkloader can write to - that's all the SQL is doing.
UUIDs exist because they were or might have been handy for something - they're just a unique(ish) identifier that can be created at any time. They're in specimen records because someone loaded them (eg, to help find stuff in iDigBio) or because something needs to or already has (or was going to but then was deleted) go in asynchronously, or maybe just because someone clicked the button to see what would happen.
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Yes, can you and Adrienne respond on which users are mammals/MSB related? Then we can get a list of what specimens they entered to try to track down the data.
On Fri, May 11, 2018 at 1:05 PM, jldunnum notifications@github.com wrote:
Mariel, let me know if there is anything you want me to help with on this. Most of the MSB users are mammals students.
Jonathan L. Dunnum Ph.D. Senior Collection Manager Division of Mammals, Museum of Southwestern Biology University of New Mexico Albuquerque, NM 87131 (505) 277-9262 Fax (505) 277-1351
MSB Mammals website: http://www.msb.unm.edu/mammals/index.html Facebook: http://www.facebook.com/MSBDivisionofMammals
Shipping Address: Museum of Southwestern Biology Division of Mammals University of New Mexico CERIA Bldg 83, Room 204 Albuquerque, NM 87131
From: Mariel Campbell notifications@github.com Sent: Friday, May 11, 2018 11:51:27 AM To: ArctosDB/arctos Cc: Jonathan Dunnum; Assign Subject: Re: [ArctosDB/arctos] Auto-upload extra identifiers, attributes from data entry (#1294)
Can I claim everything from MSB users, so I can see what is going on and how to resolve? I'm pretty sure no one else has any idea of what to do. MSB Mammals has had to create these through student data entry to accommodate extra attributes, parts, and IDs that won't fit in the standard form. They've been doing this for a couple of years, and I don't think any of the UUIDs so created have been resolved to link to the corresponding data. It would be good to figure out what records have these so we can go back and find out if data were lost and need to be re-entered.
On Fri, May 11, 2018 at 11:42 AM, dustymc notifications@github.com wrote:
Agreed in principle, but we'll never have an infinite number of tools to do the infinite number of things that can be done in Arctos!
I'm happy to help you SQL-shuffle things around - eg, if you want to "claim" everything from your users in the CSV I provided or whatever.
Or you can just go through the "claim from my users" process for each of the half-dozen things the bulkloader can write to - that's all the SQL is doing.
UUIDs exist because they were or might have been handy for something - they're just a unique(ish) identifier that can be created at any time. They're in specimen records because someone loaded them (eg, to help find stuff in iDigBio) or because something needs to or already has (or was going to but then was deleted) go in asynchronously, or maybe just because someone clicked the button to see what would happen.
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Taking a different tack on this: How do we associate UUIDs we find attached to specimens with something in the Extras bulkloader? I keep coming across these and don't know how to resolve them. This particular set is 4 years old, from before there was a clear path to upload the extras post data entry.
http://arctos.database.museum/saved/Bradley%20Tank%20Carlsbad%20MLC
That's definitely not a use case I had in mind....
select USERNAME,count(*) c ,'cf_temp_specevent' tbl from cf_temp_specevent where UUID in (select display_value from coll_obj_other_id_num where other_id_type='UUID' and collection_object_id in (select collection_object_id from flat where locality_id=10713310)) group by username
union
select USERNAME,count(*) c ,'cf_temp_parts' tbl from cf_temp_parts where other_id_number in (select display_value from coll_obj_other_id_num where other_id_type='UUID' and collection_object_id in (select collection_object_id from flat where locality_id=10713310)) group by username
union
select USERNAME,count(*) c ,'cf_temp_attributes' tbl from cf_temp_attributes where other_id_number in (select display_value from coll_obj_other_id_num where other_id_type='UUID' and collection_object_id in (select collection_object_id from flat where locality_id=10713310)) group by username
union
select USERNAME,count(*) c ,'cf_temp_oids' tbl from cf_temp_oids where EXISTING_OTHER_ID_NUMBER in (select display_value from coll_obj_other_id_num where other_id_type='UUID' and collection_object_id in (select collection_object_id from flat where locality_id=10713310)) group by username
union
select USERNAME,count(*) c ,'cf_temp_collector' tbl from cf_temp_collector where other_id_number in (select display_value from coll_obj_other_id_num where other_id_type='UUID' and collection_object_id in (select collection_object_id from flat where locality_id=10713310)) group by username
10 ;
no rows selected
probably already loaded, or whoever entered them deleted them.
Can we find all of these that are not associated with any data, so we can check against original data sheets and see if data need to be re-entered? I doubt whoever entered them deleted them, but possibly already loaded.
On Tue, Oct 23, 2018 at 9:18 PM dustymc notifications@github.com wrote:
That's definitely not a use case I had in mind....
select USERNAME,count() c ,'cf_temp_specevent' tbl from cf_temp_specevent where UUID in (select display_value from coll_obj_other_id_num where other_id_type='UUID' and collection_object_id in (select collection_object_id from flat where locality_id=10713310)) group by username union select USERNAME,count() c ,'cf_temp_parts' tbl from cf_temp_parts where other_id_number in (select display_value from coll_obj_other_id_num where other_id_type='UUID' and collection_object_id in (select collection_object_id from flat where locality_id=10713310)) group by username union select USERNAME,count() c ,'cf_temp_attributes' tbl from cf_temp_attributes where other_id_number in (select display_value from coll_obj_other_id_num where other_id_type='UUID' and collection_object_id in (select collection_object_id from flat where locality_id=10713310)) group by username union select USERNAME,count() c ,'cf_temp_oids' tbl from cf_temp_oids where EXISTING_OTHER_ID_NUMBER in (select display_value from coll_obj_other_id_num where other_id_type='UUID' and collection_object_id in (select collection_object_id from flat where locality_id=10713310)) group by username union select USERNAME,count(*) c ,'cf_temp_collector' tbl from cf_temp_collector where other_id_number in (select display_value from coll_obj_other_id_num where other_id_type='UUID' and collection_object_id in (select collection_object_id from flat where locality_id=10713310)) group by username 10 ;
no rows selected
probably already loaded, or whoever entered them deleted them.
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They're all in the daily email.
Request to have the table that displays records pending upload display an Other Identifiers field or some sort of identifier so that if there are problems we can go back to our original data records to clarify and resolve. Right now there is no way to know what specimen the part uuid is being loaded if it has not already been cataloged. If something did not get cataloged because of some data entry error or other problem, we cannot track the uuid back and figure out what went wrong. At a minimum, we would need to know the GUID prefix of the collection creating the part uuid and some identifier of the specimen in the related bulkloader.
Currently displayed fields at EnterData/Bulkloader/BrowseAndEdit-->Extras or the individual bulkloaders:
delete | STATUS | GUID | Specimen | GUID_PREFIX | OTHER_ID_TYPE | OTHER_ID_NUMBER | ATTRIBUTE | ATTRIBUTE_VALUE | ATTRIBUTE_UNITS | ATTRIBUTE_DATE | ATTRIBUTE_METH | DETERMINER | REMARKS
Example? I think I'm confused.
I don't know if this is possible, but we need some information linking the specimen in the bulkloader or the cataloged specimen with the uuid that is in the extras waiting to be loaded. Otherwise, we don't have any idea what specimen data these extras are tied to in order to track them down if they fail to load, and these data will be lost. Also, I loaded one but don't see anything showing up in the corresponding specimen record - is there a 24 delay?
The UUID is the link - that's why it exists. Examples would still be very useful.
We are accumulating many other ids, attributes etc added during data entry that need to be added throught the batch tools bulkloaders. Any way to automate or simplify this process? e.g. UUID: ac15bafc-e22a-45d5-868a-56450b947c07